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revision 1.21, Sun Feb 18 22:13:53 2007 UTC revision 1.28, Sun Sep 30 20:52:51 2007 UTC
# Line 9  Line 9 
9      use Tracer;      use Tracer;
10      use ERDBLoad;      use ERDBLoad;
11      use Stats;      use Stats;
12        use Time::HiRes qw(time);
13    
14  =head1 Custom SEED Attribute Manager  =head1 Custom SEED Attribute Manager
15    
# Line 344  Line 345 
345                                      -labels => \%labelMap,                                      -labels => \%labelMap,
346                                      -default => 'string');                                      -default => 'string');
347      # Allow the user to specify a new field name. This is required if the      # Allow the user to specify a new field name. This is required if the
348      # user has selected the "(new)" marker. We put a little scriptlet in here that      # user has selected the "(new)" marker.
     # selects the (new) marker when the user enters the field.  
     push @retVal, "<script language=\"javaScript\">";  
349      my $fieldField = "document.$name.fieldName";      my $fieldField = "document.$name.fieldName";
350      my $newName = "\"" . NewName() . "\"";      my $newName = "\"" . NewName() . "\"";
351      push @retVal, $cgi->Tr($cgi->th("New Field Name"),      push @retVal, $cgi->Tr($cgi->th("New Field Name"),
# Line 387  Line 386 
386  =head3 LoadAttributesFrom  =head3 LoadAttributesFrom
387    
388  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>  C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
389    s
390  Load attributes from the specified tab-delimited file. Each line of the file must  Load attributes from the specified tab-delimited file. Each line of the file must
391  contain an object ID in the first column, an attribute key name in the second  contain an object ID in the first column, an attribute key name in the second
392  column, and attribute values in the remaining columns. The attribute values will  column, and attribute values in the remaining columns. The attribute values will
# Line 430  Line 429 
429    
430  If specified, the specified object type will be prefixed to each object ID.  If specified, the specified object type will be prefixed to each object ID.
431    
432    =item resume
433    
434    If specified, key-value pairs already in the database will not be reinserted.
435    
436  =back  =back
437    
438  =cut  =cut
# Line 439  Line 442 
442      my ($self, $fileName, %options) = @_;      my ($self, $fileName, %options) = @_;
443      # Declare the return variable.      # Declare the return variable.
444      my $retVal = Stats->new('keys', 'values');      my $retVal = Stats->new('keys', 'values');
445        # Initialize the timers.
446        my ($insertTime, $eraseTime, $archiveTime, $checkTime) = (0, 0, 0, 0);
447      # Check for append mode.      # Check for append mode.
448      my $append = ($options{append} ? 1 : 0);      my $append = ($options{append} ? 1 : 0);
449        # Check for resume mode.
450        my $resume = ($options{resume} ? 1 : 0);
451      # Create a hash of key names found.      # Create a hash of key names found.
452      my %keyHash = ();      my %keyHash = ();
453      # Open the file for input. Note we must anticipate the possibility of an      # Open the file for input. Note we must anticipate the possibility of an
# Line 459  Line 466 
466          $ah = Open(undef, ">$options{archive}");          $ah = Open(undef, ">$options{archive}");
467          Trace("Load file will be archived to $options{archive}.") if T(3);          Trace("Load file will be archived to $options{archive}.") if T(3);
468      }      }
469      # Finally, open a database transaction.      # Insure we recover from errors.
     $self->BeginTran();  
     # Insure we recover from errors. If an error occurs, we will delete the archive file and  
     # roll back the updates.  
470      eval {      eval {
471          # Loop through the file.          # Loop through the file.
472          while (! eof $fh) {          while (! eof $fh) {
# Line 475  Line 479 
479              }              }
480              # Archive the line (if necessary).              # Archive the line (if necessary).
481              if (defined $ah) {              if (defined $ah) {
482                    my $startTime = time();
483                  Tracer::PutLine($ah, [$id, $key, @values]);                  Tracer::PutLine($ah, [$id, $key, @values]);
484                    $archiveTime += time() - $startTime;
485              }              }
486              # Do some validation.              # Do some validation.
487              if (! $id) {              if (! $id) {
# Line 488  Line 494 
494                  # An ID without a key is a serious error.                  # An ID without a key is a serious error.
495                  my $lines = $retVal->Ask('linesIn');                  my $lines = $retVal->Ask('linesIn');
496                  Confess("Line $lines in $fileName has no attribute key.");                  Confess("Line $lines in $fileName has no attribute key.");
497                } elsif (! @values) {
498                    # A line with no values is not allowed.
499                    my $lines = $retVal->Ask('linesIn');
500                    Trace("Line $lines for key $key has no attribute values.") if T(1);
501                    $retVal->Add(skipped => 1);
502              } else {              } else {
503                  # The key contains a real part and an optional sub-part. We need the real part.                  # The key contains a real part and an optional sub-part. We need the real part.
504                  my ($realKey, $subKey) = $self->SplitKey($key);                  my ($realKey, $subKey) = $self->SplitKey($key);
# Line 502  Line 513 
513                          $retVal->Add(keys => 1);                          $retVal->Add(keys => 1);
514                          # If this is NOT append mode, erase the key.                          # If this is NOT append mode, erase the key.
515                          if (! $append) {                          if (! $append) {
516                                my $startTime = time();
517                              $self->EraseAttribute($realKey);                              $self->EraseAttribute($realKey);
518                                $eraseTime += time() - $startTime;
519                                Trace("Attribute $realKey erased.") if T(3);
520                          }                          }
521                      }                      }
522                      Trace("Key $realKey found.") if T(3);                      Trace("Key $realKey found.") if T(3);
523                  }                  }
524                    # If we're in resume mode, check to see if this insert is redundant.
525                    my $ok = 1;
526                    if ($resume) {
527                        my $startTime = time();
528                        my $count = $self->GetAttributes($id, $key, @values);
529                        $ok = ! $count;
530                        $checkTime += time() - $startTime;
531                    }
532                    if ($ok) {
533                  # Everything is all set up, so add the value.                  # Everything is all set up, so add the value.
534                        my $startTime = time();
535                  $self->AddAttribute($id, $key, @values);                  $self->AddAttribute($id, $key, @values);
536                        $insertTime += time() - $startTime;
537                    } else {
538                        # Here we skipped because of resume mode.
539                        $retVal->Add(resumeSkip => 1);
540                    }
541    
542                  my $progress = $retVal->Add(values => 1);                  my $progress = $retVal->Add(values => 1);
543                  Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);                  Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
544              }              }
545          }          }
546            $retVal->Add(eraseTime   => $eraseTime);
547            $retVal->Add(insertTime  => $insertTime);
548            $retVal->Add(archiveTime => $archiveTime);
549            $retVal->Add(checkTime   => $checkTime);
550      };      };
551      # Check for an error.      # Check for an error.
552      if ($@) {      if ($@) {
553          # Here we have an error. Roll back the transaction and delete the archive file.          # Here we have an error. Display the error message.
554          my $message = $@;          my $message = $@;
555          Trace("Rolling back attribute updates due to error.") if T(1);          Trace("Error during attribute load: $message") if T(0);
556          $self->RollbackTran();          $retVal->AddMessage($message);
         if (defined $ah) {  
             Trace("Deleting archive file $options{archive}.") if T(1);  
             close $ah;  
             unlink $options{archive};  
557          }          }
558          Confess("Error during attribute load: $message");      # Close the archive file, if any.
     } else {  
         # Here the load worked. Commit the transaction and close the archive file.  
         Trace("Committing attribute upload.") if T(2);  
         $self->CommitTran();  
559          if (defined $ah) {          if (defined $ah) {
560              Trace("Closing archive file $options{archive}.") if T(2);              Trace("Closing archive file $options{archive}.") if T(2);
561              close $ah;              close $ah;
562          }          }
     }  
563      # Return the result.      # Return the result.
564      return $retVal;      return $retVal;
565  }  }
# Line 1722  Line 1747 
1747      return sort @groups;      return sort @groups;
1748  }  }
1749    
1750    =head3 QueryAttributes
1751    
1752    C<< my @attributeData = $ca->QueryAttributes($filter, $filterParms); >>
1753    
1754    Return the attribute data based on an SQL filter clause. In the filter clause,
1755    the name C<$object> should be used for the object ID, C<$key> should be used for
1756    the key name, C<$subkey> for the subkey value, and C<$value> for the value field.
1757    
1758    =over 4
1759    
1760    =item filter
1761    
1762    Filter clause in the standard ERDB format, except that the field names are C<$object> for
1763    the object ID field, C<$key> for the key name field, C<$subkey> for the subkey field,
1764    and C<$value> for the value field. This abstraction enables us to hide the details of
1765    the database construction from the user.
1766    
1767    =item filterParms
1768    
1769    Parameters for the filter clause.
1770    
1771    =item RETURN
1772    
1773    Returns a list of tuples. Each tuple consists of an object ID, a key (with optional subkey), and
1774    one or more attribute values.
1775    
1776    =back
1777    
1778    =cut
1779    
1780    # This hash is used to drive the substitution process.
1781    my %AttributeParms = (object => 'HasValueFor(to-link)',
1782                          key    => 'HasValueFor(from-link)',
1783                          subkey => 'HasValueFor(subkey)',
1784                          value  => 'HasValueFor(value)');
1785    
1786    sub QueryAttributes {
1787        # Get the parameters.
1788        my ($self, $filter, $filterParms) = @_;
1789        # Declare the return variable.
1790        my @retVal = ();
1791        # Make sue we have filter parameters.
1792        my $realParms = (defined($filterParms) ? $filterParms : []);
1793        # Create the query by converting the filter.
1794        my $realFilter = $filter;
1795        for my $name (keys %AttributeParms) {
1796            $realFilter =~ s/\$$name/$AttributeParms{$name}/g;
1797        }
1798        my $query = $self->Get(['HasValueFor'], $realFilter, $realParms);
1799        # Loop through the results, forming the output attribute tuples.
1800        while (my $result = $query->Fetch()) {
1801            # Get the four values from this query result row.
1802            my ($objectID, $key, $subkey, $value) = $result->Values([$AttributeParms{object},
1803                                                                    $AttributeParms{key},
1804                                                                    $AttributeParms{subkey},
1805                                                                    $AttributeParms{value}]);
1806            # Combine the key and the subkey.
1807            my $realKey = ($subkey ? $key . $self->{splitter} . $subkey : $key);
1808            # Split the value.
1809            my @values = split $self->{splitter}, $value;
1810            # Output the result.
1811            push @retVal, [$objectID, $realKey, @values];
1812        }
1813        # Return the result.
1814        return @retVal;
1815    }
1816    
1817  =head2 Key and ID Manipulation Methods  =head2 Key and ID Manipulation Methods
1818    
1819  =head3 ParseID  =head3 ParseID
# Line 1765  Line 1857 
1857      if ($idValue =~ /^([A-Za-z]+):(.+)/) {      if ($idValue =~ /^([A-Za-z]+):(.+)/) {
1858          # Here we have a typed ID.          # Here we have a typed ID.
1859          ($type, $id) = ($1, $2);          ($type, $id) = ($1, $2);
1860            # Fix the case sensitivity on PDB IDs.
1861            if ($type eq 'PDB') { $id = lc $id; }
1862      } elsif ($idValue =~ /fig\|/) {      } elsif ($idValue =~ /fig\|/) {
1863          # Here we have a feature ID.          # Here we have a feature ID.
1864          ($type, $id) = (Feature => $idValue);          ($type, $id) = (Feature => $idValue);
# Line 1840  Line 1934 
1934    
1935  =item RETURN  =item RETURN
1936    
1937  Returns a B<DBObject> for the attribute value's target object.  Returns a B<ERDBObject> for the attribute value's target object.
1938    
1939  =back  =back
1940    
# Line 1939  Line 2033 
2033      return $retVal;      return $retVal;
2034  }  }
2035    
2036    
2037    =head3 AttributeTable
2038    
2039    C<< my $tableHtml = CustomAttributes::AttributeTable($cgi, @attrList); >>
2040    
2041    Format the attribute data into an HTML table.
2042    
2043    =over 4
2044    
2045    =item cgi
2046    
2047    CGI query object used to generate the HTML
2048    
2049    =item attrList
2050    
2051    List of attribute results, in the format returned by the L</GetAttributes> or
2052    L</QueryAttributes> methods.
2053    
2054    =item RETURN
2055    
2056    Returns an HTML table displaying the attribute keys and values.
2057    
2058    =back
2059    
2060    =cut
2061    
2062    sub AttributeTable {
2063        # Get the parameters.
2064        my ($cgi, @attrList) = @_;
2065        # Accumulate the table rows.
2066        my @html = ();
2067        for my $attrData (@attrList) {
2068            # Format the object ID and key.
2069            my @columns = map { CGI::escapeHTML($_) } @{$attrData}[0,1];
2070            # Now we format the values. These remain unchanged unless one of them is a URL.
2071            my $lastValue = scalar(@{$attrData}) - 1;
2072            push @columns, map { $_ =~ /^http:/ ? $cgi->a({ href => $_ }, $_) : $_ } @{$attrData}[2 .. $lastValue];
2073            # Assemble the values into a table row.
2074            push @html, $cgi->Tr($cgi->td(\@columns));
2075        }
2076        # Format the table in the return variable.
2077        my $retVal = $cgi->table({ border => 2 }, $cgi->Tr($cgi->th(['Object', 'Key', 'Values'])), @html);
2078        # Return it.
2079        return $retVal;
2080    }
2081  1;  1;

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